18-47334891-T-C

Variant names:

• chr18-47334891-T-C
• rs2196180
• ENST00000586905.3:n.37+49130T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586905.3(MIR4527HG):​n.37+49130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,116 control chromosomes in the GnomAD database, including 47,292 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (47292 hom., cov: 32)
• Consequence: MIR4527HG ENST00000586905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586905.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	NR_147192.1		n.38+49130T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4527HG	ENST00000586905.3	TSL:1	n.37+49130T>C		intron	N/A
	MIR4527HG	ENST00000598649.1	TSL:3	n.73+49094T>C		intron	N/A
	MIR4527HG	ENST00000833748.1		n.408+20638T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119150 AN: 151998 Hom.: 47239 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.784 AC: 119262 AN: 152116 Hom.: 47292 Cov.: 32 AF XY: 0.786 AC XY: 58470 AN XY: 74356

African (AFR) AF: 0.896 AC: 37207 AN: 41522

American (AMR) AF: 0.696 AC: 10644 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2668 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4509 AN: 5178

South Asian (SAS) AF: 0.786 AC: 3777 AN: 4804

European-Finnish (FIN) AF: 0.828 AC: 8759 AN: 10576

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49098 AN: 67962

Other (OTH) AF: 0.756 AC: 1596 AN: 2110

Alfa AF: 0.736 Hom.: 51170

Bravo AF: 0.781

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2196180; hg19: chr18-44861262;